Fast Simulation of Facilitated Spin Models

We show how to apply the absorbing Markov chain Monte Carlo algorithm of Novotny to simulate kinetically constrained models of glasses. We consider in detail one-spin facilitated models, such as the East model and its generalizations to arbitrary dimensions. We investigate how to maximise the efficiency of the algorithms, and show that simulation times can be improved on standard continuous time Monte Carlo by several orders of magnitude. We illustrate the method with equilibrium and aging results. These include a study of relaxation times in the East model for dimensions d=1 to d=13, which provides further evidence that the hierarchical relaxation in this model is present in all dimensions. We discuss how the method can be applied to other kinetically constrained models.Comment: 8 pages, 4 figure

An analysis of internal/external event ordering strategies for COTS distributed simulation

Distributed simulation is a technique that is used to link together several models so that they can work together (or interoperate) as a single model. The High Level Architecture (HLA) (IEEE 1516.2000) is the de facto standard that defines the technology for this interoperation. The creation of a distributed simulation of models developed in COTS Simulation Packages (CSPs) is of interest. The motivation is to attempt to reduce lead times of simulation projects by reusing models that have already been developed. This paper discusses one of the issues involved in distributed simulation with CSPs. This is the issue of synchronising data sent between models with the simulation of a model by a CSP, the so-called external/internal event ordering problem. The motivation is that the particular algorithm employed can represent a significant overhead on performance

A class of pairwise models for epidemic dynamics on weighted networks

In this paper, we study the $SIS$ (susceptible-infected-susceptible) and $SIR$ (susceptible-infected-removed) epidemic models on undirected, weighted networks by deriving pairwise-type approximate models coupled with individual-based network simulation. Two different types of theoretical/synthetic weighted network models are considered. Both models start from non-weighted networks with fixed topology followed by the allocation of link weights in either (i) random or (ii) fixed/deterministic way. The pairwise models are formulated for a general discrete distribution of weights, and these models are then used in conjunction with network simulation to evaluate the impact of different weight distributions on epidemic threshold and dynamics in general. For the $SIR$ dynamics, the basic reproductive ratio $R_0$ is computed, and we show that (i) for both network models $R_{0}$ is maximised if all weights are equal, and (ii) when the two models are equally matched, the networks with a random weight distribution give rise to a higher $R_0$ value. The models are also used to explore the agreement between the pairwise and simulation models for different parameter combinations

On the Simulation of Polynomial NARMAX Models

In this paper, we show that the common approach for simulation non-linear stochastic models, commonly used in system identification, via setting the noise contributions to zero results in a biased response. We also demonstrate that to achieve unbiased simulation of finite order NARMAX models, in general, we require infinite order simulation models. The main contributions of the paper are two-fold. Firstly, an alternate representation of polynomial NARMAX models, based on Hermite polynomials, is proposed. The proposed representation provides a convenient way to translate a polynomial NARMAX model to a corresponding simulation model by simply setting certain terms to zero. This translation is exact when the simulation model can be written as an NFIR model. Secondly, a parameterized approximation method is proposed to curtail infinite order simulation models to a finite order. The proposed approximation can be viewed as a trade-off between the conventional approach of setting noise contributions to zero and the approach of incorporating the bias introduced by higher-order moments of the noise distribution. Simulation studies are provided to illustrate the utility of the proposed representation and approximation method.Comment: Accepted in IEEE CDC 201

NNVA: Neural Network Assisted Visual Analysis of Yeast Cell Polarization Simulation

Complex computational models are often designed to simulate real-world physical phenomena in many scientific disciplines. However, these simulation models tend to be computationally very expensive and involve a large number of simulation input parameters which need to be analyzed and properly calibrated before the models can be applied for real scientific studies. We propose a visual analysis system to facilitate interactive exploratory analysis of high-dimensional input parameter space for a complex yeast cell polarization simulation. The proposed system can assist the computational biologists, who designed the simulation model, to visually calibrate the input parameters by modifying the parameter values and immediately visualizing the predicted simulation outcome without having the need to run the original expensive simulation for every instance. Our proposed visual analysis system is driven by a trained neural network-based surrogate model as the backend analysis framework. Surrogate models are widely used in the field of simulation sciences to efficiently analyze computationally expensive simulation models. In this work, we demonstrate the advantage of using neural networks as surrogate models for visual analysis by incorporating some of the recent advances in the field of uncertainty quantification, interpretability and explainability of neural network-based models. We utilize the trained network to perform interactive parameter sensitivity analysis of the original simulation at multiple levels-of-detail as well as recommend optimal parameter configurations using the activation maximization framework of neural networks. We also facilitate detail analysis of the trained network to extract useful insights about the simulation model, learned by the network, during the training process.Comment: Published at IEEE Transactions on Visualization and Computer Graphic

Enabling Distributed Simulation of OMNeT++ INET Models

Parallel and distributed simulation have been extensively researched for a long time. Nevertheless, many simulation models are still executed sequentially. We attribute this to the fact that many of those models are simply not capable of being executed in parallel since they violate particular constraints. In this paper, we analyze the INET model suite, which enables network simulation in OMNeT++, with regard to parallelizability. We uncovered several issues preventing parallel execution of INET models. We analyzed those issues and developed solutions allowing INET models to be run in parallel. A case study shows the feasibility of our approach. Though there are parts of the model suite that we didn't investigate yet and the performance can still be improved, the results show parallelization speedup for most configurations. The source code of our implementation is available through our web site at code.comsys.rwth-aachen.de.Comment: Published in: A. F\"orster, C. Sommer, T. Steinbach, M. W\"ahlisch (Eds.), Proc. of 1st OMNeT++ Community Summit, Hamburg, Germany, September 2, 2014, arXiv:1409.0093, 201

Monte Carlo simulation of ice models

We propose a number of Monte Carlo algorithms for the simulation of ice models and compare their efficiency. One of them, a cluster algorithm for the equivalent three colour model, appears to have a dynamic exponent close to zero, making it particularly useful for simulations of critical ice models. We have performed extensive simulations using our algorithms to determine a number of critical exponents for the square ice and F models.Comment: 32 pages including 15 postscript figures, typeset in LaTeX2e using the Elsevier macro package elsart.cl